Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-seq

The use of Yamanaka factors or chemical compound converting mouse embryonic fibroblasts (MEFs) into induced pluripotent stem cells (iPSCs). However, these reprogramming processes are highly heterogeneous and remain poorly understood. Here we comprehensively profile the different stages of an optimized Oct4, Sox2, Klf4 and chemical-induced reprogramming at single-cell resolution. Using high efficient OSK induced reprogramming systems, which can get chimera-competent iPSCs at D7, we collected cells across 8 days reprogramming time course [1] using Fluidigm C1. In total, we analyzed 912 single cells isolated at D0, D1, D2, D3, D5, D7, D8, plus MEFs, iPSCs, and ESCs were sequenced, [2] using 10x Genomics, we analyzed 59141 single cells after QC isolated at D0, D1, D3, D5, D6, D7, D8, plus MEFs and ESCs (GSM3629847-GSM3629855). Using chemical induction of pluripotency (CIP) systems, we collected cells across 40 days reprogramming time course using 10x Genomics (GSM3619570-GSM3619581). In total, we analyzed 93585 single cells after QC isolated at D0, D3, D6, D9, D12, D16, D18, D22, D26, D32, D36, D40.